pulling-phylogeny
jt-miller
2024-01-28
Some code to look at the overall phylogenetic placement of the taxa we are modeling.
Previous literature has identified that overall trends in phenology are thought to be shared across the phylogeny for plants (i.e. evolutionary history will influence flowering). We can both: 1) Test this hypothesis in my datasets. 2) Evaluate the overall scope of the tree that we are capturing in this analysis.
Load in Packages
library(rotl) # calls the open tree api to give us a rough idea of the current phylogeny, I would still take these with a grain of salt but its not a bad exploratory option
library(data.table)
library(ggplot2)
library(stringr)
library(tidyverse)## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errorslibrary(phytools)## Loading required package: ape
##
## Attaching package: 'ape'
##
## The following object is masked from 'package:dplyr':
##
## where
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## Loading required package: maps
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## Attaching package: 'maps'
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## maplibrary(ape)Load Data
Simplify to just names and create a simple subset for illustration purposes
Grab a tree for these tips
Labeling Phylogeny
In order to address both (1) and (2), it may be helpful to label the phylogeny as a overall visual.
Create some labeled plots
New plan, new plan: Find representative taxa 1) That have the best amount of temporal coverage for year by year phenometric measurements
named_data_labeled <- fread("/home/jt-miller/Gurlab/sliding-phenology/data/processed/blooming-period-dataset.csv")
#
flowering_data <- named_data_labeled
result_table <- flowering_data %>%
group_by(speciesName, year) %>%
summarise(
condition_satisfied = n() > 5 & n_distinct(doy) >= 3
) %>%
group_by(speciesName) %>%
summarise(
num_years_condition_satisfied = sum(condition_satisfied)
)## `summarise()` has grouped output by 'speciesName'. You can override using the
## `.groups` argument.flowering_data2 <- merge(flowering_data, result_table, by = "speciesName")
flowering_data3 <- flowering_data2 %>%
filter(!bloom_period == "unknown") %>% # doesnt contribute to known phenology
group_by(speciesName) %>%
mutate(bloomSpecificity = case_when(
n_distinct(bloom_period) == 1 & bloom_period == 'spring bloomer' ~ "spring bloomer",
n_distinct(bloom_period) == 1 & bloom_period == 'fall bloomer' ~ "fall bloomer",
n_distinct(bloom_period) > 1 ~ "opportunistic bloomer"
)) %>%
distinct(speciesName, bloomSpecificity, .keep_all = TRUE)
flowering_data4 <- flowering_data3 %>%
filter(num_years_condition_satisfied >= 25)
name_subset <- flowering_data3$speciesName
resolved_subset <- tnrs_match_names(name_subset)## Warning: , Acmispon rigidus, Malacothamnus enigmaticus, Ottleya strigosa,
## Simpsonanthus jonesii are not matched# resolved_subset2 <- filter(resolved_subset, !ott_id == 5502771)
# resolved_subset2 <- filter(resolved_subset2, !ott_id == 173589)
# tree_object <- tol_induced_subtree(ott_ids = ott_id(resolved_subset2)) # appends lineages from open tree
in_tree <- is_in_tree(ott_id(resolved_subset))
in_tree## Abronia villosa Senegalia greggii
## TRUE TRUE
## Acalypha californica Acamptopappus sphaerocephalus
## TRUE TRUE
## Achyronychia cooperi Acmispon americanus
## TRUE TRUE
## Acmispon argophyllus Acmispon glaber
## TRUE TRUE
## Acmispon heermannii Lotus salsuginosus
## TRUE TRUE
## Acmispon micranthus Acmispon strigosus
## TRUE TRUE
## Adenophyllum porophylloides Agave deserti
## TRUE TRUE
## Aliciella latifolia Allionia incarnata
## TRUE TRUE
## Allium fimbriatum Allium monticola
## TRUE TRUE
## Allium peninsulare Amaranthus fimbriatus
## TRUE TRUE
## Ambrosia acanthicarpa Ambrosia dumosa
## TRUE TRUE
## Ambrosia salsola Amsinckia intermedia
## TRUE TRUE
## Amsinckia menziesii Amsinckia tessellata
## TRUE TRUE
## Antirrhinum filipes Aphyllon cooperi
## TRUE TRUE
## Arctostaphylos glauca Argemone munita
## TRUE TRUE
## Aristida adscensionis Aristida purpurea
## TRUE TRUE
## Artemisia ludoviciana Asclepias albicans
## TRUE TRUE
## Asclepias subulata Astragalus aridus
## TRUE TRUE
## Astragalus coccineus Astragalus crotalariae
## TRUE TRUE
## Astragalus didymocarpus Astragalus douglasii
## TRUE TRUE
## Astragalus lentiginosus Astragalus nuttallianus
## TRUE TRUE
## Astragalus palmeri Astragalus tricarinatus
## TRUE TRUE
## Atrichoseris platyphylla Atriplex canescens
## TRUE TRUE
## Atriplex hymenelytra Atriplex polycarpa
## TRUE TRUE
## Ayenia compacta Baccharis brachyphylla
## TRUE TRUE
## Baccharis salicifolia Bahiopsis parishii
## TRUE TRUE
## Baileya multiradiata Baileya pauciradiata
## TRUE TRUE
## Bebbia juncea Bernardia incana
## TRUE TRUE
## Boechera johnstonii Boerhavia coccinea
## TRUE TRUE
## Boerhavia coulteri Boerhavia triquetra
## TRUE TRUE
## Boerhavia wrightii Bouteloua aristidoides
## TRUE TRUE
## Bouteloua barbata Echinopepon bigelovii
## TRUE TRUE
## Brassica tournefortii Brickellia atractyloides
## TRUE TRUE
## Brickellia frutescens Bromus berteroanus
## TRUE TRUE
## Bromus madritensis Bromus tectorum
## TRUE TRUE
## Hoffmannseggia microphylla Cistanthe ambigua
## TRUE TRUE
## Calandrinia ciliata var. menziesii Calochortus concolor
## TRUE TRUE
## Calochortus dunnii Calochortus palmeri
## TRUE TRUE
## Calycoseris parryi Calycoseris wrightii
## TRUE TRUE
## Calyptridium monandrum Camissonia brevipes
## TRUE FALSE
## Eulobus californicus Camissonia cardiophylla
## TRUE FALSE
## Chylismia claviformis Camissonia pallida
## TRUE FALSE
## Eremothera refracta Camissoniopsis bistorta
## TRUE TRUE
## Camissoniopsis confusa Camissoniopsis pallida
## TRUE TRUE
## Castilleja exserta Castilleja foliolosa
## TRUE TRUE
## Castilleja minor Streptanthus cooperi
## TRUE TRUE
## Caulanthus hallii Caulanthus lasiophyllus
## TRUE TRUE
## Caulanthus simulans Ceanothus perplexans
## TRUE FALSE
## Cenchrus setaceus Centaurea melitensis
## TRUE TRUE
## Cercocarpus betuloides Chaenactis artemisiifolia
## TRUE TRUE
## Chaenactis carphoclinia Chaenactis fremontii
## TRUE TRUE
## Chaenactis glabriuscula Chaenactis stevioides
## TRUE TRUE
## Euphorbia polycarpa Chenopodiastrum murale
## TRUE TRUE
## Chenopodiastrum murale Chilopsis linearis
## TRUE TRUE
## Chorizanthe brevicornu Chorizanthe corrugata
## TRUE TRUE
## Chorizanthe fimbriata Chorizanthe rigida
## TRUE TRUE
## Chylismia brevipes Chylismia cardiophylla
## TRUE TRUE
## Chylismia claviformis Cistanthe ambigua
## TRUE TRUE
## Claytonia parviflora Cleomella arborea
## TRUE TRUE
## Cleomella arborea Cleomella obtusifolia
## TRUE TRUE
## Coleogyne ramosissima Condea emoryi
## TRUE TRUE
## Corethrogyne filaginifolia Crassula connata
## TRUE TRUE
## Crossosoma bigelovii Croton californicus
## TRUE TRUE
## Johnstonella angustifolia Cryptantha barbigera
## TRUE TRUE
## Johnstonella holoptera Cryptantha decipiens
## TRUE TRUE
## Cryptantha ganderi Cryptantha intermedia
## TRUE TRUE
## Cryptantha maritima Eremocarya micrantha
## TRUE TRUE
## Cryptantha muricata Cryptantha nevadensis
## TRUE TRUE
## Cryptantha pterocarya Cryptantha racemosa
## TRUE TRUE
## Cryptantha utahensis Cucurbita palmata
## TRUE TRUE
## Cuscuta californica Cuscuta psorothamnensis
## TRUE TRUE
## Cylindropuntia bigelovii Cylindropuntia echinocarpa
## TRUE TRUE
## Cylindropuntia fosbergii Cylindropuntia ganderi
## TRUE TRUE
## Cylindropuntia ramosissima Dalea mollis
## TRUE TRUE
## Dalea mollissima Datura discolor
## TRUE TRUE
## Datura wrightii Delphinium parishii
## TRUE TRUE
## Dendromecon rigida Descurainia pinnata
## TRUE TRUE
## Dicoria canescens Dimorphotheca sinuata
## TRUE TRUE
## Diplacus bigelovii Diplacus calycinus
## TRUE TRUE
## Dichelostemma capitatum Ditaxis lanceolata
## TRUE TRUE
## Ditaxis serrata Ditaxis serrata
## TRUE TRUE
## Dithyrea californica Tomostima cuneifolia
## TRUE TRUE
## Dudleya pulverulenta Dudleya lanceolata
## TRUE TRUE
## Dudleya saxosa Echinocereus engelmannii
## TRUE TRUE
## Ehrendorferia chrysantha Emmenanthe penduliflora
## TRUE TRUE
## Encelia actoni Encelia farinosa
## TRUE FALSE
## Encelia frutescens Ephedra aspera
## TRUE TRUE
## Epilobium canum Epipactis gigantea
## TRUE TRUE
## Eremalche exilis Eremalche rotundifolia
## TRUE TRUE
## Eremocarya lepida Eremocarya micrantha
## TRUE TRUE
## Eremothera boothii Eremothera chamaenerioides
## TRUE TRUE
## Eremothera refracta Eriastrum densifolium
## TRUE TRUE
## Eriastrum diffusum Eriastrum eremicum
## TRUE TRUE
## Ericameria brachylepis Ericameria linearifolia
## TRUE TRUE
## Ericameria paniculata Conyza bonariensis
## TRUE TRUE
## Erigeron canadensis Eriodictyon crassifolium
## TRUE TRUE
## Eriodictyon trichocalyx Eriogonum deflexum
## TRUE TRUE
## Eriogonum elongatum Eriogonum fasciculatum
## TRUE TRUE
## Eriogonum gracile Eriogonum inflatum
## TRUE TRUE
## Eriogonum pusillum Eriogonum reniforme
## TRUE TRUE
## Eriogonum thomasii Eriogonum thurberi
## TRUE TRUE
## Eriogonum trichopes Eriogonum wrightii
## TRUE TRUE
## Eriophyllum ambiguum Eriophyllum confertiflorum
## TRUE TRUE
## Eriophyllum wallacei Erodium cicutarium
## TRUE TRUE
## Erodium texanum Erythranthe cardinalis
## TRUE TRUE
## Erythranthe floribunda Erythranthe guttata
## TRUE TRUE
## Erythranthe parishii Eschscholzia androuxii
## TRUE TRUE
## Eschscholzia californica Eschscholzia minutiflora
## TRUE TRUE
## Eschscholzia papastillii Eschscholzia parishii
## TRUE TRUE
## Eucrypta chrysanthemifolia Eucrypta micrantha
## TRUE TRUE
## Eulobus californicus Euphorbia abramsiana
## TRUE TRUE
## Euphorbia arizonica Euphorbia eriantha
## TRUE TRUE
## Euphorbia melanadenia Euphorbia micromera
## TRUE TRUE
## Euphorbia pediculifera Euphorbia polycarpa
## TRUE TRUE
## Euphorbia setiloba Eustoma exaltatum
## TRUE TRUE
## Fagonia laevis Fagonia pachyacantha
## TRUE TRUE
## Ferocactus cylindraceus Festuca bromoides
## TRUE TRUE
## Festuca octoflora Fouquieria splendens
## TRUE TRUE
## Funastrum cynanchoides Funastrum cynanchoides
## TRUE TRUE
## Funastrum hirtellum Galium angustifolium
## TRUE TRUE
## Galium stellatum Geraea canescens
## TRUE TRUE
## Gilia angelensis Gilia capitata
## TRUE TRUE
## Gilia scopulorum Gilia stellata
## TRUE TRUE
## Gutierrezia californica Gutierrezia sarothrae
## TRUE TRUE
## Helianthus annuus Helianthus petiolaris
## TRUE TRUE
## Heliotropium curassavicum Hesperocallis undulata
## TRUE TRUE
## Hesperoyucca whipplei Hibiscus denudatus
## TRUE TRUE
## Hilaria rigida Hirschfeldia incana
## TRUE TRUE
## Hoffmannseggia microphylla Hordeum murinum
## TRUE TRUE
## Horsfordia newberryi Hulsea vestita
## TRUE TRUE
## Ambrosia salsola Condea emoryi
## TRUE TRUE
## Isocoma acradenia Cleomella arborea
## TRUE TRUE
## Johnstonella angustifolia Johnstonella costata
## TRUE TRUE
## Cryptantha racemosa Juncus bufonius
## TRUE TRUE
## Justicia californica Kallstroemia californica
## TRUE TRUE
## Keckiella antirrhinoides Krameria bicolor
## TRUE TRUE
## Krameria erecta Krameria grayi
## TRUE TRUE
## Langloisia setosissima Larrea tridentata
## TRUE TRUE
## Lasthenia coronaria Lasthenia gracilis
## TRUE TRUE
## Layia glandulosa Lepidium fremontii
## TRUE TRUE
## Lepidium lasiocarpum Lepidospartum squamatum
## TRUE TRUE
## Leptosiphon chrysanthus Leptosiphon lemmonii
## TRUE TRUE
## Leptosyne bigelovii Leptosyne californica
## TRUE TRUE
## Lilium parryi Linanthus dianthiflorus
## TRUE TRUE
## Linanthus jonesii Linanthus maculatus
## TRUE TRUE
## Loeflingia squarrosa Langloisia matthewsii
## TRUE TRUE
## Loeseliastrum schottii Filago arizonica
## TRUE TRUE
## Filago depressa Filago californica
## TRUE TRUE
## Lotus scoparius Lotus strigosus
## TRUE TRUE
## Bromus tomentellus Lupinus arizonicus
## TRUE TRUE
## Lupinus bicolor Lupinus concinnus
## TRUE TRUE
## Lupinus hirsutissimus Lupinus shockleyi
## TRUE TRUE
## Lupinus sparsiflorus Lupinus truncatus
## TRUE TRUE
## Lycium andersonii Lycium brevipes
## TRUE TRUE
## Lycium cooperi Lycium fremontii
## TRUE TRUE
## Lyrocarpa coulteri Lythrum californicum
## TRUE TRUE
## Malacothamnus fasciculatus Malacothrix glabrata
## TRUE TRUE
## Malacothrix stebbinsii Malva parviflora
## TRUE TRUE
## Mammillaria dioica Marah macrocarpa
## TRUE TRUE
## Marina parryi Medicago lupulina
## TRUE TRUE
## Medicago polymorpha Melica frutescens
## TRUE TRUE
## Melica imperfecta Melilotus albus
## TRUE TRUE
## Melilotus indicus Mentzelia affinis
## TRUE TRUE
## Mentzelia albicaulis Mentzelia desertorum
## TRUE TRUE
## Mentzelia hirsutissima Mentzelia involucrata
## TRUE TRUE
## Mentzelia jonesii Mesembryanthemum nodiflorum
## TRUE TRUE
## Mimetanthe pilosa Diplacus bigelovii
## TRUE TRUE
## Mirabilis laevis Mirabilis multiflora
## TRUE TRUE
## Mirabilis tenuiloba Mohavea confertiflora
## TRUE TRUE
## Monoptilon bellioides Muhlenbergia microsperma
## TRUE TRUE
## Muilla maritima Nama demissa
## TRUE TRUE
## Nama hispida Nasturtium officinale
## TRUE TRUE
## Prosopis glandulosa Spiranthes odorata
## TRUE TRUE
## Nemacladus glanduliferus Nemacladus orientalis
## TRUE TRUE
## Nemacladus rubescens Nemacladus tenuis
## TRUE TRUE
## Nemophila menziesii Neogaerrhinum filipes
## TRUE TRUE
## Nicotiana attenuata Nicotiana clevelandii
## TRUE TRUE
## Nicotiana glauca Nicotiana obtusifolia
## TRUE TRUE
## Nicotiana quadrivalvis Nolina bigelovii
## TRUE TRUE
## Nolina parryi Oenothera deltoides
## TRUE TRUE
## Oenothera elata Oligomeris linifolia
## TRUE TRUE
## Olneya tesota Oncosiphon piluliferus
## TRUE TRUE
## Oncosiphon piluliferus Opuntia basilaris
## TRUE TRUE
## Opuntia phaeacantha Aphyllon cooperi
## TRUE TRUE
## Palafoxia arida Pappostipa speciosa
## TRUE TRUE
## Parietaria hespera Parkinsonia aculeata
## TRUE TRUE
## Parkinsonia florida Pectis papposa
## TRUE TRUE
## Pectocarya anisocarpa Pectocarya heterocarpa
## TRUE TRUE
## Pectocarya linearis Pectocarya peninsularis
## TRUE TRUE
## Pectocarya platycarpa Pectocarya recurvata
## TRUE TRUE
## Pectocarya setosa Cenchrus setaceus
## TRUE TRUE
## Penstemon californicus Penstemon centranthifolius
## TRUE TRUE
## Penstemon clevelandii Cleomella arborea
## TRUE TRUE
## Perityle emoryi Petalonyx thurberi
## TRUE TRUE
## Peucephyllum schottii Phacelia crenulata
## TRUE TRUE
## Phacelia brachyloba Phacelia campanularia
## TRUE TRUE
## Phacelia cicutaria Phacelia crenulata
## TRUE TRUE
## Phacelia cryptantha Phacelia distans
## TRUE TRUE
## Phacelia ivesiana Phacelia minor
## TRUE TRUE
## Phacelia neglecta Phacelia pedicellata
## TRUE TRUE
## Phacelia ramosissima Phacelia rotundifolia
## TRUE TRUE
## Phalaris minor Pholisma arenarium
## TRUE TRUE
## Pholistoma membranaceum Phoradendron californicum
## TRUE TRUE
## Physalis crassifolia Physaria tenella
## TRUE TRUE
## Pilostyles thurberi Plagiobothrys arizonicus
## TRUE TRUE
## Plantago ovata Plantago patagonica
## TRUE TRUE
## Hilaria rigida Pleurocoronis pluriseta
## TRUE TRUE
## Pluchea sericea Poa secunda
## TRUE TRUE
## Polypogon monspeliensis Porophyllum gracile
## TRUE TRUE
## Proboscidea altheifolia Prosopis glandulosa
## TRUE TRUE
## Prunus fasciculata Prunus fremontii
## TRUE TRUE
## Psathyrotes ramosissima Pseudognaphalium biolettii
## TRUE TRUE
## Pseudoziziphus parryi Psorothamnus arborescens
## TRUE TRUE
## Psorothamnus emoryi Psorothamnus schottii
## TRUE TRUE
## Psorothamnus spinosus Pterostegia drymarioides
## TRUE TRUE
## Pulicaria paludosa Rafinesquia californica
## TRUE TRUE
## Rafinesquia neomexicana Rhus aromatica
## TRUE TRUE
## Rhus ovata Ribes indecorum
## TRUE TRUE
## Salix exigua Salix gooddingii
## TRUE TRUE
## Salix laevigata Salsola paulsenii
## TRUE TRUE
## Salsola tragus Saltugilia australis
## TRUE TRUE
## Saltugilia latimeri Salvia apiana
## TRUE TRUE
## Salvia carduacea Salvia columbariae
## FALSE TRUE
## Salvia eremostachya Salvia greatae
## TRUE TRUE
## Salvia vaseyi Sambucus nigra subsp. caerulea
## FALSE TRUE
## Funastrum cynanchoides Schismus arabicus
## TRUE TRUE
## Schismus barbatus Scrophularia californica
## TRUE TRUE
## Scutellaria mexicana Senecio californicus
## TRUE TRUE
## Senecio mohavensis Senegalia greggii
## TRUE TRUE
## Senna armata Senna artemisioides
## TRUE TRUE
## Senna covesii Sesuvium verrucosum
## TRUE TRUE
## Sidotheca emarginata Simmondsia chinensis
## TRUE TRUE
## Sisymbrium irio Sisymbrium orientale
## TRUE TRUE
## Solanum douglasii Solanum parishii
## TRUE TRUE
## Solanum umbelliferum Solidago velutina
## TRUE TRUE
## Sonchus asper Sonchus oleraceus
## TRUE TRUE
## Sphaeralcea ambigua Stanleya pinnata
## TRUE TRUE
## Stemodia durantifolia Stephanomeria exigua
## TRUE TRUE
## Stephanomeria pauciflora Stillingia linearifolia
## TRUE TRUE
## Stillingia spinulosa Stipa capensis
## TRUE TRUE
## Stipa hymenoides Pappostipa speciosa
## TRUE TRUE
## Streptanthella longirostris Streptanthella longirostris
## TRUE TRUE
## Stylocline gnaphaloides Tamarix aphylla
## TRUE TRUE
## Tamarix ramosissima Tetracoccus fasciculatus
## TRUE TRUE
## Thamnosma montana Caulanthus lasiophyllus
## TRUE TRUE
## Thymophylla pentachaeta Thysanocarpus curvipes
## TRUE TRUE
## Tidestromia oblongifolia Tidestromia suffruticosa
## FALSE TRUE
## Tiquilia canescens Tiquilia palmeri
## TRUE TRUE
## Tiquilia plicata Tomostima cuneifolia
## TRUE TRUE
## Trianthema portulacastrum Tribulus terrestris
## TRUE TRUE
## Trichoptilium incisum Trixis californica
## TRUE TRUE
## Tropidocarpum gracile Uropappus lindleyi
## TRUE TRUE
## Veronica anagallis-aquatica Volutaria tubuliflora
## TRUE TRUE
## Xylorhiza cognata Xylorhiza orcuttii
## TRUE TRUE
## Xylorhiza tortifolia Yucca schidigera
## TRUE TRUE
## Zeltnera venusta Pseudoziziphus parryi
## TRUE TRUEtr <- tol_induced_subtree(ott_id(resolved_subset)[in_tree])##
Progress [--------------------------------] 0/1935 ( 0%) ?s
Progress [============================] 1935/1935 (100%) 0s
## Warning in collapse_singles(tr, show_progress): Dropping singleton nodes with
## labels: Magnoliopsida ott99252, mrcaott2ott2645, mrcaott2ott35778,
## Mesangiospermae ott5298374, mrcaott2ott10930, mrcaott2ott969, mrcaott2ott62529,
## mrcaott2ott8379, eudicotyledons ott431495, Gunneridae ott853757,
## mrcaott2ott8384, mrcaott2ott1479, mrcaott2ott345, Malpighiales ott429482,
## mrcaott345ott22364, mrcaott345ott18689, mrcaott345ott177705,
## mrcaott345ott38722, mrcaott345ott24237, mrcaott345ott30307, mrcaott345ott26478,
## mrcaott345ott191443, mrcaott345ott485790, Euphorbieae ott520955,
## mrcaott345ott1030065, mrcaott8051ott28703, mrcaott8051ott30309,
## mrcaott33275ott41973, mrcaott33275ott402542, mrcaott33275ott334199,
## mrcaott33275ott33286, Euphorbia sect. Poinsettia ott5147152, Euphorbia subsect.
## Erianthae ott5147154, mrcaott42861ott253647, mrcaott42861ott42866,
## mrcaott42861ott343513, mrcaott42861ott124900, mrcaott376444ott1005185,
## mrcaott42868ott72820, mrcaott716894ott7056399, mrcaott550766ott989270,
## mrcaott30323ott34866, mrcaott504ott36284, mrcaott504ott10167,
## mrcaott10167ott241549, mrcaott10167ott64672, mrcaott10167ott52218,
## mrcaott52218ott764979, mrcaott52218ott262937, Bernardia (genus in kingdom
## Archaeplastida) ott523028, mrcaott30317ott209327, mrcaott30317ott72561,
## mrcaott72561ott147420, mrcaott147420ott610290, mrcaott147420ott230733,
## mrcaott147420ott190669, mrcaott147420ott402227, mrcaott147420ott816389,
## Acalypha ott560972, mrcaott170575ott211956, mrcaott6748ott423256,
## mrcaott6748ott30319, mrcaott6748ott6752, mrcaott6752ott362813,
## mrcaott6752ott174819, mrcaott6752ott671151, mrcaott6752ott6762,
## mrcaott6762ott16262, mrcaott6762ott19547, mrcaott6762ott592498,
## mrcaott6762ott6764, mrcaott6762ott426179, mrcaott6762ott24605,
## mrcaott6762ott16264, mrcaott16264ott16279, mrcaott16264ott426168,
## mrcaott3949ott15752, mrcaott3949ott28711, Picrodendraceae ott62391,
## mrcaott28711ott28714, mrcaott28714ott788306, Tetracoccus (genus in domain
## Eukaryota) ott33336, mrcaott3853ott8858, mrcaott8858ott33097,
## mrcaott8858ott12186, mrcaott8858ott98085, Salicaceae ott530183,
## mrcaott8858ott270454, mrcaott8858ott703490, mrcaott8858ott33085,
## mrcaott8858ott102531, mrcaott8858ott502530, mrcaott8858ott737360,
## mrcaott8858ott474976, Saliceae ott509390, mrcaott86747ott895191,
## mrcaott86747ott531336, mrcaott531336ott725903, mrcaott725903ott738780,
## mrcaott725903ott795555, mrcaott164187ott164212, mrcaott164212ott567279,
## mrcaott567279ott786842, mrcaott567279ott567287, mrcaott567279ott738777,
## mrcaott371ott63303, mrcaott371ott42100, mrcaott371ott22991, Urticaceae
## ott658494, mrcaott22991ott23000, mrcaott22991ott266711, mrcaott22991ott431744,
## mrcaott431744ott723994, mrcaott431744ott472752, Parietaria ott630640,
## mrcaott773ott137975, Rhamnaceae ott329916, Pseudoziziphus ott7056810, Rosaceae
## ott208036, Amygdaloideae ott731134, mrcaott10421ott156934,
## mrcaott156934ott295908, Kerrieae ott901804, mrcaott538527ott817076, Coleogyne
## ott817078, mrcaott34671ott244226, mrcaott61998ott1012886,
## mrcaott61998ott132521, mrcaott61998ott1018655, mrcaott61998ott990519,
## mrcaott61998ott946407, Dryadoideae ott366727, mrcaott122440ott207997,
## mrcaott122440ott653075, mrcaott653075ott7056984, mrcaott2511ott32687,
## mrcaott2511ott253321, mrcaott2511ott29878, Cucurbitaceae ott1006267,
## mrcaott2511ott4028, mrcaott2511ott2972, mrcaott2511ott376422,
## mrcaott2511ott351037, mrcaott2511ott14789, mrcaott2511ott14774,
## mrcaott2511ott182773, mrcaott2511ott185940, mrcaott2511ott132044,
## mrcaott2511ott2520, mrcaott2520ott14778, mrcaott2520ott11772, Cucurbiteae
## ott77740, mrcaott11772ott84409, mrcaott84409ott337509, mrcaott84409ott841310,
## mrcaott84409ott841300, Cucurbita (genus in kingdom Archaeplastida) ott379277,
## Sicyoeae ott462358, mrcaott4000ott103106, mrcaott4000ott67706,
## mrcaott4000ott10298, mrcaott10298ott870455, mrcaott10298ott103086,
## mrcaott103086ott103110, Marah ott1066441, mrcaott198664ott212996, Echinopepon
## ott198658, mrcaott309341ott337493, mrcaott309341ott760212, Apodanthaceae
## ott167651, Pilostyles ott809744, Fabales ott956360, mrcaott579ott179386,
## Fabaceae ott560323, mrcaott579ott730, mrcaott579ott45621, mrcaott579ott8603,
## Papilionoideae ott39538, mrcaott579ott5468, mrcaott579ott5457,
## mrcaott579ott5462, mrcaott579ott5470, mrcaott579ott5091, mrcaott579ott5515,
## mrcaott579ott38037, mrcaott579ott7223, mrcaott579ott11248,
## mrcaott11248ott11254, mrcaott11248ott120275, mrcaott11248ott25572,
## mrcaott11248ott75662, mrcaott11248ott24174, mrcaott11248ott11252,
## mrcaott11248ott192321, mrcaott11248ott24170, mrcaott11248ott11264,
## mrcaott11248ott24172, mrcaott11250ott314143, mrcaott11250ott62867,
## mrcaott11250ott11262, mrcaott11250ott62865, mrcaott11250ott132250,
## mrcaott11250ott11258, mrcaott11258ott752495, mrcaott11258ott532649,
## mrcaott11258ott279712, mrcaott11258ott532657, mrcaott11258ott583880,
## mrcaott363910ott462258, mrcaott462258ott563646, mrcaott462258ott596943,
## mrcaott1749ott496549, mrcaott1749ott222250, mrcaott1749ott27613,
## mrcaott1749ott38031, mrcaott38031ott42707, Medicago ott1086823,
## mrcaott38031ott209352, mrcaott38031ott424990, mrcaott38031ott525750,
## mrcaott38031ott170192, mrcaott38031ott193971, mrcaott38031ott760436,
## mrcaott38031ott193970, mrcaott38032ott646077, mrcaott38032ott374489,
## mrcaott38032ott950610, mrcaott38042ott139477, mrcaott38042ott230316,
## mrcaott38042ott262308, mrcaott38042ott1007989, mrcaott38042ott989938,
## mrcaott38042ott771616, mrcaott368370ott1072867, mrcaott34386ott72192,
## mrcaott34386ott253732, mrcaott34386ott42465, mrcaott42465ott1001097,
## mrcaott449763ott526191, mrcaott449763ott931832, Robinieae ott563850,
## mrcaott37541ott114493, mrcaott37541ott688634, Olneya ott688641,
## mrcaott3942ott82511, dalbergioids sensu lato ott7055847, Amorpheae ott615877,
## mrcaott3942ott763790, mrcaott189642ott334591, Marina ott918581,
## mrcaott189643ott189644, mrcaott189643ott920345, mrcaott240355ott240366,
## mrcaott240366ott1090116, mrcaott240366ott240370, mrcaott341195ott763792,
## mrcaott341195ott763784, mrcaott5473ott26267, mrcaott5473ott590008,
## mrcaott5473ott46797, mrcaott5473ott165471, mrcaott5473ott8026,
## mrcaott8026ott33311, mrcaott8026ott31847, Genisteae ott1090346,
## mrcaott8026ott62394, mrcaott8026ott908606, mrcaott8026ott224618,
## mrcaott8026ott398890, mrcaott8026ott8519, mrcaott8519ott726487, Lupinus
## ott878988, mrcaott8519ott222530, mrcaott8519ott388496, mrcaott8519ott553518,
## mrcaott8519ott857028, mrcaott8519ott222528, mrcaott8519ott282245,
## mrcaott282245ott902823, mrcaott902823ott1065704, mrcaott185311ott539267,
## mrcaott265614ott857024, mrcaott265634ott740409, mrcaott265634ott792139,
## mrcaott265634ott282243, mrcaott282243ott940870, mrcaott2644ott112865,
## mrcaott2644ott30537, mrcaott2644ott86941, mrcaott2644ott333121,
## mrcaott2644ott33732, mrcaott2644ott72925, mrcaott2644ott72932,
## mrcaott72932ott87429, mrcaott87429ott471741, mrcaott87429ott471728,
## mrcaott87429ott471732, Hoffmannseggia ott702632, mrcaott321621ott517678,
## mrcaott321621ott896099, mrcaott896099ott923019, mrcaott21759ott946962,
## mrcaott21759ott170059, mrcaott21759ott124017, Senna ott404633,
## mrcaott21759ott68521, mrcaott21759ott148479, mrcaott21759ott68517,
## mrcaott21759ott148477, mrcaott21759ott147099, mrcaott21759ott326851,
## mrcaott21759ott234461, mrcaott21759ott148490, mrcaott68511ott335063,
## mrcaott68511ott234453, mrcaott234453ott757700, mrcaott757700ott808767,
## mrcaott757700ott757709, mrcaott757700ott908908, mrcaott8605ott87214,
## mrcaott8605ott220379, mrcaott8605ott40823, mrcaott8605ott308458,
## mrcaott8605ott659681, mrcaott8605ott26386, mrcaott8613ott472478,
## mrcaott8613ott66199, mrcaott8613ott66193, mrcaott8613ott981814,
## mrcaott8878ott17129, mrcaott8878ott61940, mrcaott61940ott444652,
## mrcaott444652ott479055, mrcaott39645ott65125, mrcaott39645ott233743,
## mrcaott39645ott471736, mrcaott39645ott39654, mrcaott39654ott39656,
## mrcaott39658ott366575, mrcaott366575ott452957, mrcaott444638ott879743,
## Zygophylloideae ott518751, mrcaott2737ott159002, mrcaott2737ott158973,
## mrcaott2737ott158965, mrcaott2737ott760110, mrcaott2738ott2742, Larreoideae
## ott518759, mrcaott199325ott359651, mrcaott199325ott250015, Larrea ott185819,
## mrcaott250015ott414990, mrcaott87296ott462596, mrcaott87296ott199322,
## Tribuloideae ott518754, mrcaott1091855ott3902318, Krameriaceae ott1074652,
## mrcaott464458ott596333, mrcaott464458ott464459, mrcaott571539ott595139,
## mrcaott595139ott1091#ape::plot.phylo(tr, cex = 1.5, type = "phylogram") # edges are being a pain...seems the whole tree was pruned...yayPlotting
ott_ids <- tr[[2]]
ott_ids <- gsub("[^0-9 ]", "", ott_ids)
ott_names <- gsub("\\d+", "", tr[[2]])
ott_names <- gsub("\\_ott", "", ott_names)
ott_names <- gsub("_", " ", ott_names)
tree_df <- data.frame(ott_ids, ott_names)
tree_df <- tree_df %>%
rename(speciesName = ott_names)
result_df <- tree_df %>%
left_join(flowering_data3, by = "speciesName")
trait_df <- result_df
#resolved_subset_m <- merge(resolved_tr_subset, flowering_data3, by.x = "unique_name", by.y = "speciesName")
#trait_df <- merge(tree_df, flowering_data3, by.x = "ott_names", by.y = "speciesName",)
tr # try storing the list into this tree objM##
## Phylogenetic tree with 473 tips and 360 internal nodes.
##
## Tip labels:
## Euphorbia_eriantha_ott776654, Euphorbia_abramsiana_ott42861, Euphorbia_pediculifera_ott1005185, Euphorbia_arizonica_ott42868, Euphorbia_polycarpa_ott72822, Euphorbia_micromera_ott989270, ...
## Node labels:
## Spermatophyta ott10218, mrcaott2ott121, mrcaott2ott2441, Pentapetalae ott5316182, mrcaott2ott2464, rosids ott1008296, ...
##
## Rooted; no branch lengths.# Sort the merged dataframe based on the order of ott_names in tree_df
trait_df <- trait_df[order(match(trait_df$speciesName, tree_df$speciesName)), ]
trait_df <- select(result_df, ott_ids, speciesName, bloomSpecificity, num_years_condition_satisfied)
trait_df <- trait_df %>%
mutate(bloomCol = case_when(
is.na(bloomSpecificity) ~ "grey",
bloomSpecificity == "spring bloomer" ~ "darkgreen",
bloomSpecificity == "fall bloomer" ~ "darkred",
bloomSpecificity == "opportunistic bloomer" ~ "goldenrod"
))
#ordered_trait_vector <- trait_df$bloomCol[order(match(trait_df$ott_names, trait_df$ott_names))]
tr$traits <- trait_df$bloomCol
ape::plot.phylo(tr, cex = 1.5, type = "phylogram", tip.color = tr$traits) # edges are being a pain...
How do the phenometrics look?
# trait_df <- trait_df %>%
# mutate(phenometric_scope =
# case_when(
# num_years_condition_satisfied < 10 ~ "grey",
# num_years_condition_satisfied >= 10 & num_years_condition_satisfied < 20 ~ "steelblue",
# num_years_condition_satisfied >= 20~ "purple",
# TRUE ~ "pink"
#
# ))
#
# ape::plot.phylo(tr, cex = 1.5, type = "phylogram", tip.color = trait_df$phenometric_scope) # edges are being a pain...Some sample data for the package ape